: I think that it's just a holographic representation of the index. The Master
: Chief inserted the Index into it's little slot on the control panel, so
: Cortana would have to have removed it physically. What I always thought
: she did with it was absorb it into herself.

I think she whisped it away to somewhere secure enough to allow them time to destroy the reactors and /really/ ensure that Halo isn't activated. Perhaps the POA?